Abstract We use new and published detrital zircon U‐Pb data ( n > 10,000) from Oligocene‐Pliocene strata of intermontane basins of the western Colombian Andes and surrounding regions to study the evolution of sedimentary systems during the transition from arc collision/accretion to subduction. Our database indicates a shift from a compartmentalized basin architecture, locally fed by transverse drainages, toward one with enhanced connectivity and longitudinal sediment dispersal during the Middle‐Late Miocene. These events were accompanied by the end of local marine influence on depocenters and the progressive uplift of the flanking Colombian Cordilleras as they became continuous topographic features. Post‐Pliocene local and transient disruption of longitudinal rivers was caused by damming and valley‐filling, attributed to volcaniclastic flows. We interpret the inherent segmentation of strike‐slip faults and their morphological expressions as the primary controls on depocenter evolution during Early‐Middle Miocene arc collision/accretion. The subsequent transition to subduction and the tectonic segmentation of the continental margin triggered asymmetrical basin inversion in the western Colombian Andes. The modern rugged morphology in the northern intermontane region is arguably associated with widespread uplift due to upper plate cooling and strengthening by shallow subduction of the Coiba microplate. Conversely, the wide and flat morphology of aggradational basins in the southern intermontane area is interpreted as the result of incomplete inversion and the dominance of strike‐slip tectonics. The “normal” subduction of the Malpelo microplate beneath southern Colombia might be linked to a higher heat flow and localized deformation in the intra‐ and back‐arc regions.